PCAtools (version 1.3.6)

screeplot: screeplot

Description

Draw a SCREE plot, showing the distribution of explained variance across all or select principal components / eigenvectors.

Usage

screeplot(pcaobj,
  components = getComponents(pcaobj),
  xlim = NULL,
  ylim = c(0, 100),
  xlab = 'Principal component',
  xlabAngle = 90,
  xlabhjust = 0.5,
  xlabvjust = 0.5,
  ylab = 'Explained variation (%)',
  ylabAngle = 0,
  ylabhjust = 0.5,
  ylabvjust = 0.5,
  axisLabSize = 16,
  title = 'SCREE plot',
  subtitle = '',
  caption = '',
  titleLabSize = 16,
  subtitleLabSize = 12,
  captionLabSize = 12,
  colBar = 'dodgerblue',
  drawCumulativeSumLine = TRUE,
  colCumulativeSumLine = 'red2',
  sizeCumulativeSumLine = 1.5,
  drawCumulativeSumPoints = TRUE,
  colCumulativeSumPoints = 'red2',
  sizeCumulativeSumPoints = 2.0,
  hline = NULL,
  hlineType = 'longdash',
  hlineCol = 'black',
  hlineWidth = 0.4,
  vline = NULL,
  vlineType = 'longdash',
  vlineCol = 'black',
  vlineWidth = 0.4,
  gridlines.major = TRUE,
  gridlines.minor = TRUE,
  borderWidth = 0.8,
  borderColour = 'black',
  returnPlot = TRUE)

Arguments

pcaobj

Object of class 'pca' created by pca(). REQUIRED.

components

The principal components to be included in the plot. DEFAULT = getComponents(pcaobj). OPTIONAL.

xlim

Limits of the x-axis. DEFAULT = NULL. OPTIONAL.

ylim

Limits of the y-axis. DEFAULT = c(0, 100). OPTIONAL.

xlab

Label for x-axis. DEFAULT = 'Principal component'. OPTIONAL.

xlabAngle

Rotation angle of x-axis labels. DEFAULT = 90. OPTIONAL.

xlabhjust

Horizontal adjustment of x-axis labels. DEFAULT = 0.5. OPTIONAL.

xlabvjust

Vertical adjustment of x-axis labels. DEFAULT = 0.5. OPTIONAL.

ylab

Label for y-axis. DEFAULT = 'Explained variation (%)'. OPTIONAL.

ylabAngle

Rotation angle of y-axis labels. DEFAULT = 0. OPTIONAL.

ylabhjust

Horizontal adjustment of y-axis labels. DEFAULT = 0.5. OPTIONAL.

ylabvjust

Vertical adjustment of y-axis labels. DEFAULT = 0.5. OPTIONAL.

axisLabSize

Size of x- and y-axis labels. DEFAULT = 16. OPTIONAL.

title

Plot title. DEFAULT = 'SCREE plot'. OPTIONAL.

subtitle

Plot subtitle. DEFAULT = ''. OPTIONAL.

caption

Plot caption. DEFAULT = ''. OPTIONAL.

titleLabSize

Size of plot title. DEFAULT = 16. OPTIONAL.

subtitleLabSize

Size of plot subtitle. DEFAULT = 12. OPTIONAL.

captionLabSize

Size of plot caption. DEFAULT = 12. OPTIONAL.

colBar

DEFAULT = 'dodgerblue'. OPTIONAL.

drawCumulativeSumLine

Logical, indicating whether or not to overlay plot with a cumulative explained variance line. DEFAULT = TRUE. OPTIONAL.

colCumulativeSumLine

Colour of cumulative explained variance line. DEFAULT = 'red2'. OPTIONAL.

sizeCumulativeSumLine

Size of cumulative explained variance line. DEFAULT = 1.5. OPTIONAL.

drawCumulativeSumPoints

Logical, indicating whether or not to draw the cumulative explained variance points. DEFAULT = TRUE. OPTIONAL.

colCumulativeSumPoints

Colour of cumulative explained variance points. DEFAULT = 'red2'. OPTIONAL.

sizeCumulativeSumPoints

Size of cumulative explained variance points. DEFAULT = 2.0. OPTIONAL.

hline

Draw one or more horizontal lines passing through this/these values on y-axis. For single values, only a single numerical value is necessary. For multiple lines, pass these as a vector, e.g., c(60,90). DEFAULT = NULL. OPTIONAL.

hlineType

Line type for hline ('blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash', 'twodash'). DEFAULT = 'longdash'. OPTIONAL.

hlineCol

Colour of hline. DEFAULT = 'black'. OPTIONAL.

hlineWidth

Width of hline. DEFAULT = 0.4. OPTIONAL.

vline

Draw one or more vertical lines passing through this/these values on x-axis. For single values, only a single numerical value is necessary. For multiple lines, pass these as a vector, e.g., c(60,90). DEFAULT = NULL. OPTIONAL.

vlineType

Line type for vline ('blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash', 'twodash'). DEFAULT = 'longdash'. OPTIONAL.

vlineCol

Colour of vline. DEFAULT = 'black'. OPTIONAL.

vlineWidth

Width of vline. DEFAULT = 0.4. OPTIONAL.

gridlines.major

Logical, indicating whether or not to draw major gridlines. DEFAULT = TRUE. OPTIONAL.

gridlines.minor

Logical, indicating whether or not to draw minor gridlines. DEFAULT = TRUE. OPTIONAL.

borderWidth

Width of the border on the x and y axes. DEFAULT = 0.8. OPTIONAL.

borderColour

Colour of the border on the x and y axes. DEFAULT = 'black'. OPTIONAL.

returnPlot

Logical, indicating whether or not to return the plot object. DEFAULT = TRUE. OPTIONAL.

Value

A ggplot2 object.

Examples

# NOT RUN {
  options(scipen=10)
  options(digits=6)

  col <- 20
  row <- 20000
  mat1 <- matrix(
    rexp(col*row, rate = 0.1),
    ncol = col)
  rownames(mat1) <- paste0('gene', 1:nrow(mat1))
  colnames(mat1) <- paste0('sample', 1:ncol(mat1))

  mat2 <- matrix(
    rexp(col*row, rate = 0.1),
    ncol = col)
  rownames(mat2) <- paste0('gene', 1:nrow(mat2))
  colnames(mat2) <- paste0('sample', (ncol(mat1)+1):(ncol(mat1)+ncol(mat2)))

  mat <- cbind(mat1, mat2)

  metadata <- data.frame(row.names = colnames(mat))
  metadata$Group <- rep(NA, ncol(mat))
  metadata$Group[seq(1,40,2)] <- 'A'
  metadata$Group[seq(2,40,2)] <- 'B'
  metadata$CRP <- sample.int(100, size=ncol(mat), replace=TRUE)
  metadata$ESR <- sample.int(100, size=ncol(mat), replace=TRUE)

  p <- pca(mat, metadata = metadata, removeVar = 0.1)

  screeplot(p)

  screeplot(p, hline = 80)
# }